Structure calculations
This protocol is extracted from research article:
Encoding canonical DNA quadruplex structure
Sci Adv, Aug 31, 2018; DOI: 10.1126/sciadv.aat3007

Distance-restrained structure determinations were carried out using distance constraints from the NMR data. Calculations were performed using XPLOR-NIH (41) using the CHARMM force field and adapted for restrained MD (rMD) for nucleic acids. All calculations were executed in vacuo without explicit counterions. Typically, the distance geometry and simulated annealing refinement protocol started from 3000 different structures randomized over all dihedral angles. A number of structures did usually emerge with the same fold and separated from nonconverged structures by large gaps in components of the potential energy function (dihedral angles, van der Waals, NOE violations, and covalent geometry). These sets were subsequently submitted to rMD calculations, performed using random velocities fitting a Maxwell-Boltzmann distribution. The empirical energy function was developed for nucleic acids and treated all hydrogens explicitly. It consisted of energy terms for hydrogen bonding, nonbonded interactions, bonds, bond angles, torsion angles, and tetrahedral and planar geometry, including van der Waals and electrostatic forces. During these computations, both the glycosidic torsion angle χ and planarity restraints were imposed during computations. The final procedure consisted of a total of 53 ps of rMD, including 7 ps of 14 ps from 300 to 1000 K, a 20-ps scale-up of restraints at high temperature, 14 ps of cooling to 300 K, and 12 ps of equilibration rMD, without planarity restraints. The temperature was controlled by coupling the molecules to a temperature bath with a coupling constant of 0.025 ps. The van der Waals term was approximated using the Lennard-Jones potential energy function, and bond lengths involving hydrogens were fixed with the SHAKE algorithm. NOE, dihedral angle restraints, and chemical shifts were deposited in the Biological Magnetic Resonance Bank (BMRB), and structure coordinates have been deposited in the PDB with identification codes 5J4P, 5J05, 5J4W, 5J6U, 2M6W, 2M6V, and 2MFT, as well as in the BMRB with identification codes 30055, 30045, 30056, 30058, 19159, 19158, and 19571, respectively. Structural restraints are shown in tables S8 to S14.

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